We have several parts we want to prototype. When the parts go into production they will be injection molded clear polycarb. Is there a material selection we can get to get a completely clear (even if not optically correct) part?

You can sand then polish Transparent Detail material to a fine gloss. It will have a yellow hue but it will be fairly clear. Be generous with wall thickness since you would be removing a lot of material. I would start around 4mm and work it down to about 3mm.

You can't dictate the build orientation at Shapeways, so your parts might be built with lots of 'foggy' areas caused by contact with the support material. That shouldn't be too much of a problem if you're building lens-like objects, it'll just require a bit more time spent sanding & polishing.

- For even more money you can hire a full-service agency like FineLine Prototyping. You'll have to request a custom quote, but they'll build the part in water-clear material, polish it for you, and apply a clear lacquer for a perfect finish. http://www.finelineprototyping.com/

If more people request there is more chance of it becoming a reality on Shapeways.

Would you be interested if we offered it 'un polished' and you had to make it clear yourselves? This would make it much easier for us to calculate a pricing structure that would be fair to all rather than those with simple models to polish carrying the burden of those with models that are much more difficult (read small and fragile)..

I think a clear material would be great. If I look at my workscope, model railroading, then there is a demand for window inserts. The models itself could be done in 3D printing or with other materials, but there is the problem with the windows. You can try to cut transparent polysterol sheets, or you can work with some fluids like Kristal Klear form Microscale.
But this doesn't work for all windows, so a clear material would be fantastic. The minimum wall thickness should therefor not be higher than 1mm.
The polishing can be done by the costumers I would say. But perhaps an optional polishing service for people who don't self want to do this.